class Experiment < ActiveRecord::Base include ArchivableModel, SearchableModel belongs_to :project, inverse_of: :experiments belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User' belongs_to :last_modified_by, foreign_key: :last_modified_by_id, class_name: 'User' belongs_to :archived_by, foreign_key: :archived_by_id, class_name: 'User' belongs_to :restored_by, foreign_key: :restored_by_id, class_name: 'User' has_many :my_modules, inverse_of: :experiment, dependent: :destroy has_many :my_module_groups, inverse_of: :experiment, dependent: :destroy has_many :report_elements, inverse_of: :experiment, dependent: :destroy has_attached_file :workflowimg validates_attachment :workflowimg, content_type: { content_type: ['image/png'] }, if: :workflowimg_check auto_strip_attributes :name, :description, nullify: false validates :name, length: { minimum: Constants::NAME_MIN_LENGTH, maximum: Constants::NAME_MAX_LENGTH }, uniqueness: { scope: :project, case_sensitive: false } validates :description, length: { maximum: Constants::TEXT_MAX_LENGTH } validates :project, presence: true validates :created_by, presence: true validates :last_modified_by, presence: true with_options if: :archived do |experiment| experiment.validates :archived_by, presence: true experiment.validates :archived_on, presence: true end scope :is_archived, ->(is_archived) { where("archived = ?", is_archived) } def self.search(user, include_archived, query = nil, page = 1) project_ids = Project .search(user, include_archived, nil, Constants::SEARCH_NO_LIMIT) .select('id') if query a_query = query.strip .gsub("_","\\_") .gsub("%","\\%") .split(/\s+/) .map {|t| "%" + t + "%" } else a_query = query end if include_archived new_query = Experiment .where(project: project_ids) .where_attributes_like([:name, :description], a_query) else new_query = Experiment .is_archived(false) .where(project: project_ids) .where_attributes_like([:name, :description], a_query) end # Show all results if needed if page == Constants::SEARCH_NO_LIMIT new_query else new_query .limit(Constants::SEARCH_LIMIT) .offset((page - 1) * Constants::SEARCH_LIMIT) end end def modules_without_group MyModule.where(experiment_id: id).where(my_module_group: nil) .where(archived: false) end def active_module_groups self.my_module_groups.joins(:my_modules) .where('my_modules.archived = ?', false) .distinct end def active_modules my_modules.where(:archived => false) end def archived_modules my_modules.where(:archived => true) end def assigned_samples Sample.joins(:my_modules).where(my_modules: {id: my_modules} ) end def unassigned_samples(assigned_samples) Sample.where(organization_id: organization).where.not(id: assigned_samples) end def update_canvas( to_archive, to_add, to_rename, to_move, to_move_groups, to_clone, connections, positions, current_user, module_groups ) cloned_modules = [] begin Experiment.transaction do # First, add new modules new_ids, cloned_pairs, originals = add_modules( to_add, to_clone, current_user) cloned_modules = cloned_pairs.collect { |mn, _| mn } # Rename modules rename_modules(to_rename) # Add activities that modules were created originals.each do |m| Activity.create( type_of: :create_module, user: current_user, project: self.project, my_module: m, message: I18n.t( "activities.create_module", user: current_user.full_name, module: m.name ) ) end # Add activities that modules were cloned cloned_pairs.each do |mn, mo| Activity.create( type_of: :clone_module, project: mn.experiment.project, my_module: mn, user: current_user, message: I18n.t( "activities.clone_module", user: current_user.full_name, module_new: mn.name, module_original: mo.name ) ) end # Then, archive modules that need to be archived archive_modules(to_archive, current_user) # Update connections, positions & module group variables # with actual IDs retrieved from the new modules creation updated_to_move = {} to_move.each do |id, value| updated_to_move[new_ids.fetch(id, id)] = value end updated_to_move_groups = {} to_move_groups.each do |ids, value| mapped = [] ids.each do |id| mapped << new_ids.fetch(id, id) end updated_to_move_groups[mapped] = value end updated_connections = [] connections.each do |a,b| updated_connections << [new_ids.fetch(a, a), new_ids.fetch(b, b)] end updated_positions = Hash.new positions.each do |id, pos| updated_positions[new_ids.fetch(id, id)] = pos end updated_module_groups = {} module_groups.each do |id, name| updated_module_groups[new_ids.fetch(id, id)] = name end # Update connections update_module_connections(updated_connections) # Update module positions (no validation needed here) update_module_positions(updated_positions) # Normalize module positions normalize_module_positions # Finally, update module groups update_module_groups(updated_module_groups, current_user) # Finally move any modules to another experiment move_modules(updated_to_move) # Everyhing is set, now we can move any module groups move_module_groups(updated_to_move_groups) end rescue ActiveRecord::ActiveRecordError, ArgumentError, ActiveRecord::RecordNotSaved return false end return true end # This method generate the workflow image and saves it as # experiment attachment def generate_workflow_img require 'graphviz' graph = GraphViz.new(:G, type: :digraph, use: :neato) graph[:size] = '4,4' graph.node[color: Constants::COLOR_ALTO, style: :filled, fontcolor: Constants::COLOR_EMPEROR, shape: 'circle', fontname: 'Arial', fontsize: '16.0'] graph.edge[color: Constants::COLOR_ALTO] label = '' subg = {} # Draw orphan modules if modules_without_group modules_without_group.each do |my_module| graph .subgraph(rank: 'same') .add_nodes("Orphan-#{my_module.id}", label: label, pos: "#{my_module.x / 10},-#{my_module.y / 10}!") end end # Draw grouped modules if my_module_groups.many? my_module_groups.each_with_index do |group, gindex| subgraph_name = "cluster-#{gindex}" subg[subgraph_name] = graph.subgraph(rank: 'same') group.ordered_modules.each_with_index do |my_module, index| if my_module.outputs.any? parent = subg[subgraph_name] .add_nodes("#{subgraph_name}-#{index}", label: label, pos: "#{my_module.x / 10},-#{my_module.y / 10}!") my_module.outputs.each_with_index do |output, i| child_mod = MyModule.find_by_id(output.input_id) child_node = subg[subgraph_name] .add_nodes("#{subgraph_name}-O#{child_mod.id}-#{i}", label: label, pos: "#{child_mod.x / 10},-#{child_mod.y / 10}!") subg[subgraph_name].add_edges(parent, child_node) end elsif my_module.inputs.any? parent = subg[subgraph_name] .add_nodes("#{subgraph_name}-#{index}", label: label, pos: "#{my_module.x / 10},-#{my_module.y / 10}!") my_module.inputs.each_with_index do |input, i| child_mod = MyModule.find_by_id(input.output_id) child_node = subg[subgraph_name] .add_nodes("#{subgraph_name}-I#{child_mod.id}-#{i}", label: label, pos: "#{child_mod.x / 10},-#{child_mod.y / 10}!") subg[subgraph_name].add_edges(child_node, parent) end end end end else my_module_groups.each do |group| group.ordered_modules.each_with_index do |my_module, index| if my_module.outputs.any? parent = graph.add_nodes("N-#{index}", label: label, pos: "#{my_module.x / 10},-#{ my_module.y / 10}!") my_module.outputs.each_with_index do |output, i| child_mod = MyModule.find_by_id(output.input_id) child_node = graph .add_nodes("N-O#{child_mod.id}-#{i}", label: label, pos: "#{child_mod.x / 10},-#{child_mod.y / 10}!") graph.add_edges(parent, child_node) end elsif my_module.inputs.any? parent = graph.add_nodes("N-#{index}", label: label, pos: "#{my_module.x / 10},-#{my_module.y / 10}!") my_module.inputs.each_with_index do |input, i| child_mod = MyModule.find_by_id(input.output_id) child_node = graph .add_nodes("N-I#{child_mod.id}-#{i}", label: label, pos: "#{child_mod.x / 10},-#{child_mod.y / 10}!") graph.add_edges(child_node, parent) end end end end end file_location = Tempfile.open(['wimg', '.png'], Rails.root.join('tmp')) graph.output(png: file_location.path) begin file = File.open(file_location) self.workflowimg = file file.close save touch(:workflowimg_updated_at) rescue => ex logger.error ex.message end end # Clone this experiment to given project def deep_clone_to_project(current_user, project) # First we have to find unique name for our little experiment experiment_names = project.experiments.map(&:name) format = 'Clone %d - %s' i = 1 i += 1 while experiment_names.include?(format(format, i, name)) clone = Experiment.new( name: format(format, i, name), description: description, created_by: current_user, last_modified_by: current_user, project: project ) # Copy all workflows my_module_groups.each do |g| clone.my_module_groups << g.deep_clone_to_experiment(current_user, clone) end # Copy modules without group clone.my_modules << modules_without_group.map do |m| m.deep_clone_to_experiment(current_user, clone) end clone.save # Create workflow image clone.delay.generate_workflow_img clone end def move_to_project(project) self.project = project my_modules.each do |m| new_tags = [] m.tags.each do |t| new_tags << t.deep_clone_to_project(project) end m.my_module_tags.destroy_all project.tags << new_tags m.tags << new_tags end result = save touch(:workflowimg_updated_at) if result result end # Get projects where user is either owner or user in the same organization # as this experiment def projects_with_role_above_user(current_user) organization = project.organization projects = organization.projects.where(archived: false) current_user.user_projects .where(project: projects) .where('role < 2') .map(&:project) end # Projects to which this experiment can be moved (inside the same # organization and not archived), all users assigned on experiment.project has # to be assigned on such project def moveable_projects(current_user) projects = projects_with_role_above_user(current_user) projects = projects.each_with_object([]) do |p, arr| arr << p if (project.users - p.users).empty? arr end projects - [project] end private # Archive all modules. Receives an array of module integer IDs. def archive_modules(module_ids) module_ids.each do |m_id| my_module = self.my_modules.find_by_id(m_id) unless my_module.blank? my_module.archive! end end modules.reload end # Archive all modules. Receives an array of module integer IDs and current user. def archive_modules(module_ids, current_user) module_ids.each do |m_id| my_module = self.my_modules.find_by_id(m_id) unless my_module.blank? my_module.archive!(current_user) end end my_modules.reload end # Add modules, and returns a map of "virtual" IDs with # actual IDs of saved modules. # to_add is an array of hashes, each containing 'name', # 'x', 'y' and 'id'. # to_clone is a hash, storing new cloned modules as keys, # and original modules as values. def add_modules(to_add, to_clone, current_user) originals = [] cloned_pairs = {} ids_map = Hash.new to_add.each do |m| original = MyModule.find_by_id(to_clone.fetch(m[:id], nil)) if original.present? then my_module = original.deep_clone(current_user) cloned_pairs[my_module] = original else my_module = MyModule.new( experiment: self) originals << my_module end my_module.name = m[:name] my_module.x = m[:x] my_module.y = m[:y] my_module.created_by = current_user my_module.last_modified_by = current_user my_module.save! ids_map[m[:id]] = my_module.id.to_s end my_modules.reload return ids_map, cloned_pairs, originals end # Rename modules; this method accepts a map where keys # represent IDs of modules, and values new names for # such modules. If a module with given ID doesn't exist, # it's obviously not updated. def rename_modules(to_rename) to_rename.each do |id, new_name| my_module = MyModule.find_by_id(id) if my_module.present? my_module.name = new_name my_module.save! end end end # Move modules; this method accepts a map where keys # represent IDs of modules, and values represent experiment # IDs of new names to which the given modules should be moved. # If a module with given ID doesn't exist (or experiment ID) # it's obviously not updated. Any connection on module is destroyed. def move_modules(to_move) to_move.each do |id, experiment_id| my_module = my_modules.find_by_id(id) experiment = project.experiments.find_by_id(experiment_id) next unless my_module.present? && experiment.present? my_module.experiment = experiment # Calculate new module position new_pos = my_module.get_new_position my_module.x = new_pos[:x] my_module.y = new_pos[:y] unless my_module.outputs.destroy_all && my_module.inputs.destroy_all raise ActiveRecord::ActiveRecordError end my_module.save end # Generate workflow image for the experiment in which we moved the task generate_workflow_img_for_moved_modules(to_move) end # Move module groups; this method accepts a map where keys # represent IDs of modules which are in module group, # and values represent experiment # IDs of new names to which the given module group should be moved. # If a module with given ID doesn't exist (or experiment ID) # it's obviously not updated. Position for entire module group is updated # to bottom left corner. def move_module_groups(to_move) to_move.each do |ids, experiment_id| modules = my_modules.where(id: ids) groups = Set.new(modules.map(&:my_module_group)) experiment = project.experiments.find_by_id(experiment_id) groups.each do |group| next unless group && experiment.present? # Find the lowest point for current modules(max_y) and the leftmost # module(min_x) if experiment.active_modules.empty? max_y = 0 min_x = 0 else max_y = experiment.active_modules.maximum(:y) + MyModule::HEIGHT min_x = experiment.active_modules.minimum(:x) end # Set new positions curr_min_x = modules.min_by(&:x).x curr_min_y = modules.min_by(&:y).y modules.each { |m| m.x += -curr_min_x + min_x } modules.each { |m| m.y += -curr_min_y + max_y } modules.each do |m| m.experiment = experiment m.save! end group.experiment = experiment group.save! end end # Generate workflow image for the experiment in which we moved the workflow generate_workflow_img_for_moved_modules(to_move) end # Generates workflow img when the workflow or module is moved # to other experiment def generate_workflow_img_for_moved_modules(to_move) to_move.values.uniq.each do |id| experiment = Experiment.find_by_id(id) next unless experiment experiment.delay.generate_workflow_img end end # Update connections for all modules in this project. # Input is an array of arrays, where first element represents # source node, and second element represents target node. # Example input: [ [1, 2], [2, 3], [4, 5], [2, 5] ] def update_module_connections(connections) require 'rgl/base' require 'rgl/adjacency' require 'rgl/topsort' dg = RGL::DirectedAdjacencyGraph.new connections.each do |a,b| # Check if both vertices exist if (my_modules.find_all {|m| [a.to_i, b.to_i].include? m.id }).count == 2 dg.add_edge(a, b) end end # Check if cycles exist! topsort = dg.topsort_iterator.to_a if topsort.length == 0 and dg.edges.size > 1 raise ArgumentError, "Cycles exist." end # First, delete existing connections # but keep a copy of previous state previous_sources = {} previous_sources.default = [] my_modules.each do |m| previous_sources[m.id] = [] m.inputs.each do |c| previous_sources[m.id] << c.from end end self.my_modules.each do |m| unless m.outputs.destroy_all raise ActiveRecord::ActiveRecordError end end # Add new connections filtered_edges = dg.edges.collect { |e| [e.source, e.target] } filtered_edges.each do |a, b| Connection.create!(:input_id => b, :output_id => a) end # Unassign samples from former downstream modules # for all destroyed connections unassign_samples_from_old_downstream_modules(previous_sources) visited = [] # Assign samples to all new downstream modules filtered_edges.each do |a, b| source = self.my_modules.find(a.to_i) target = self.my_modules.find(b.to_i) # Do this only for new edges if previous_sources[target.id].exclude?(source) # Go as high upstream as new edges take us # and then assign samples to all downsteam samples assign_samples_to_new_downstream_modules(previous_sources, visited, source) end end # Save topological order of modules (for modules without workflow, # leave them unordered) self.my_modules.each do |m| if topsort.include? m.id.to_s m.workflow_order = topsort.find_index(m.id.to_s) else m.workflow_order = -1 end m.save! end # Make sure to reload my modules, which now have updated connections and samples self.my_modules.reload true end # When connections are deleted, unassign samples that # are not inherited anymore def unassign_samples_from_old_downstream_modules(sources) self.my_modules.each do |my_module| sources[my_module.id].each do |s| # Only do this for newly deleted connections if s.outputs.map{|i| i.to}.exclude? my_module my_module.get_downstream_modules.each do |dm| # Get unique samples for all upstream modules um = dm.get_upstream_modules um.shift # remove current module ums = um.map{|m| m.samples}.flatten.uniq s.samples.each do |sample| dm.samples.delete(sample) if ums.exclude? sample end end end end end end # Assign samples to new connections recursively def assign_samples_to_new_downstream_modules(sources, visited, my_module) # If samples are already assigned for this module, stop going upstream if visited.include? (my_module) return end visited << my_module # Edge case, when module is source or it doesn't have any new input connections if my_module.inputs.blank? or ( my_module.inputs.map{|c| c.from} - sources[my_module.id] ).empty? my_module.get_downstream_modules.each do |dm| new_samples = my_module.samples.select { |el| dm.samples.exclude?(el) } dm.samples.push(*new_samples) end else my_module.inputs.each do |input| # Go upstream for new in connections if sources[my_module.id].exclude?(input.from) assign_samples_to_new_downstream_modules(input.from) end end end end # Updates positions of modules. # Input is a map where keys are module IDs, and values are # hashes like { x: , y: }. def update_module_positions(positions) positions.each do |id, pos| unless MyModule.update(id, x: pos[:x], y: pos[:y]) raise ActiveRecord::ActiveRecordError end end self.my_modules.reload end # Normalize module positions in this project. def normalize_module_positions # This method normalizes module positions so x-s and y-s # are all positive x_diff = (self.my_modules.collect { |m| m.x }).min y_diff = (self.my_modules.collect { |m| m.y }).min self.my_modules.each do |m| unless m.update_attribute(:x, m.x - x_diff) and m.update_attribute(:y, m.y - y_diff) raise ActiveRecord::ActiveRecordError end end end # Recalculate module groups in this project. Input is # a hash of module ids and their corresponding module names. def update_module_groups(module_groups, current_user) require 'rgl/base' require 'rgl/adjacency' require 'rgl/connected_components' dg = RGL::DirectedAdjacencyGraph[] group_ids = Set.new active_modules.each do |m| unless m.my_module_group.blank? group_ids << m.my_module_group.id end unless dg.has_vertex? m.id dg.add_vertex m.id end m.outputs.each do |o| dg.add_edge m.id, o.to.id end end workflows = [] dg.to_undirected.each_connected_component { |w| workflows << w } # Retrieve maximum allowed module group name max_length = (MyModuleGroup.validators_on(:name).select { |v| v.class == ActiveModel::Validations::LengthValidator }).first.options[:maximum] # For each workflow, generate new names new_index = 1 wf_names = [] suffix = I18n.t("my_module_groups.new.suffix") cut_index = -(suffix.length + 1) workflows.each do |w| modules = MyModule.find(w) # Get an array of module names names = [] modules.each do |m| names << module_groups.fetch(m.id.to_s, "") end names = names.uniq name = (names.select { |v| v != "" }).join(", ") if w.length <= 1 name = nil elsif name.blank? name = I18n.t("my_module_groups.new.name", index: new_index) new_index += 1 while MyModuleGroup.find_by(name: name).present? name = I18n.t("my_module_groups.new.name", index: new_index) new_index += 1 end elsif name.length > max_length # If length is too long, shorten it name = name[0..(max_length + cut_index)] + suffix end wf_names << name end # Remove any existing module groups from modules unless MyModuleGroup.destroy_all(:id => group_ids.to_a) raise ActiveRecord::ActiveRecordError end # Second, create new groups workflows.each_with_index do |w, i| # Single modules are not considered part of any workflow if w.length > 1 group = MyModuleGroup.new( name: wf_names[i], experiment: self, my_modules: MyModule.find(w)) group.created_by = current_user group.save! end end my_module_groups.reload true end def workflowimg_check workflowimg_content_type rescue false end end